ABSTRACT Crohn?s disease (CD), one of the major forms of Inflammatory Bowel Disease (IBD), is a complex disorder marked by chronic relapsing inflammation driven by CD4+ T helper 1 (TH1) cells that can affect any part of the gastrointestinal tract. CD is thought to result from an inappropriate mucosal immune response to the intestinal microbiota in genetically susceptible individuals. Consistent with this notion, CD patients harbor a dysbiotic microbiota. However, it remains unclear if the CD-associated dysbiosis plays a casual role or is secondary to inflammation. More than 100 loci predispose to CD of which polymorphisms in NOD2 are the strongest known genetic risk factor for disease development in adult and pediatric onset CD. However, the great majority of individuals homozygous for NOD2 CD-associated variants do not develop CD and no spontaneous intestinal inflammation mimicking CD occurs in Nod2?/? mice or knockin mice homozygous for the CD-associated L1007insC NOD2 variant. These findings suggest that additional genetic and/or environmental factors are critical for disease development. We found that combined, but not single deficiency, of NOD2 and phagocyte NAPDH oxidase activity triggers early-onset spontaneous TH1-type intestinal inflammation in mice with the pathological and immune hallmarks of CD. Development of disease required the presence of Mucispirillum schaedleri, a Gram-negative anaerobic bacterium that is an inhabitant of the colonic mucus layer of normal mice. The absence of NOD2 and CYBB led to marked accumulation of Mucispirillum in the gut which was associated with impaired recruitment of neutrophils and killing of the bacterium by luminal neutrophils. Mutant mice were protected from disease by maternal immunoglobulins against Mucispirillum during breastfeeding. These results indicate that a specific intestinal microbe can trigger CD-like disease in the presence of impaired clearance of the bacterium by innate immunity. We hypothesize that NOD2 and the NAPDH oxidase regulate the susceptibility to CD by controlling the abundance and local invasion of specific pathobionts such as Mucispirillum. We further hypothesize that killing of specific microbes by neutrophils regulated via NOD2 and NAPDH oxidase is important to prevent the development of CD-like disease. Finally, we hypothesize that targeting colitis-causing pathobionts such as Mucispirillum using diet could be an approach to treat CD-like colitis. In this grant application, we propose three specific Aims to understand the role of NOD2 and phagocyte NAPDH oxidase in the regulation of the microbiota and induction of colitis using a new animal model that exhibit pathology and immune alterations characteristic of CD.